[English] 日本語
Yorodumi
- PDB-5yit: Crystal Structure of Hypothetical protein (Rv3272) from Mycobacte... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yit
TitleCrystal Structure of Hypothetical protein (Rv3272) from Mycobacterium tuberculosis
ComponentsCoA transferase III
KeywordsTRANSFERASE / CoA transferase Family III / interlocked dimer / Mycobacterium tuberculosis / Rv3272
Function / homologyTransferases; Transferring sulfur-containing groups; CoA-transferases / CoA-transferase family III domain 3 superfamily / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III / transferase activity / Probable fatty acyl-CoA transferase Rv3272
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsKarade, S.S. / Pratap, J.V.
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2019
Title: Rv3272 encodes a novel Family III CoA transferase that alters the cell wall lipid profile and protects mycobacteria from acidic and oxidative stress.
Authors: Karade, S.S. / Pandey, S. / Ansari, A. / Das, S. / Tripathi, S. / Arora, A. / Chopra, S. / Pratap, J.V. / Dasgupta, A.
History
DepositionOct 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_volume ..._audit_author.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CoA transferase III
B: CoA transferase III
C: CoA transferase III
D: CoA transferase III
E: CoA transferase III


Theoretical massNumber of molelcules
Total (without water)212,5275
Polymers212,5275
Non-polymers00
Water2,576143
1
A: CoA transferase III
B: CoA transferase III


Theoretical massNumber of molelcules
Total (without water)85,0112
Polymers85,0112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11080 Å2
ΔGint-84 kcal/mol
Surface area26470 Å2
MethodPISA
2
C: CoA transferase III
D: CoA transferase III


Theoretical massNumber of molelcules
Total (without water)85,0112
Polymers85,0112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11240 Å2
ΔGint-81 kcal/mol
Surface area26650 Å2
MethodPISA
3
E: CoA transferase III

E: CoA transferase III


Theoretical massNumber of molelcules
Total (without water)85,0112
Polymers85,0112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10670 Å2
ΔGint-80 kcal/mol
Surface area27150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)542.400, 71.000, 49.550
Angle α, β, γ (deg.)90.00, 90.44, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16B
26E
17C
27D
18C
28E
19D
29E

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEUAA6 - 3916 - 391
21PROPROLEULEUBB6 - 3916 - 391
12ASNASNLEULEUAA5 - 3915 - 391
22ASNASNLEULEUCC5 - 3915 - 391
13ASNASNPHEPHEAA5 - 3905 - 390
23ASNASNPHEPHEDD5 - 3905 - 390
14PROPROLEULEUBB6 - 3916 - 391
24PROPROLEULEUCC6 - 3916 - 391
15PROPROPHEPHEBB6 - 3906 - 390
25PROPROPHEPHEDD6 - 3906 - 390
16PROPROVALVALBB6 - 3896 - 389
26PROPROVALVALEE6 - 3896 - 389
17ASNASNPHEPHECC5 - 3905 - 390
27ASNASNPHEPHEDD5 - 3905 - 390
18PROPROVALVALCC6 - 3896 - 389
28PROPROVALVALEE6 - 3896 - 389
19PROPROVALVALDD6 - 3896 - 389
29PROPROVALVALEE6 - 3896 - 389

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.226724, -0.973914, 0.009409), (-0.973952, 0.226677, -0.00584), (0.003555, -0.010488, -0.999939)132.05688, 105.1132, 36.26708
3given(0.94819, -0.317665, -0.004977), (0.317672, 0.9482, 0.000801), (0.004465, -0.00234, 0.999987)44.73596, 8.95089, 9.00563
4given(-0.520532, -0.853794, 0.009066), (-0.853841, 0.52052, -0.003866), (-0.001418, -0.009753, -0.999951)113.03493, 63.5233, 27.20017
5given(-0.785528, -0.618786, 0.007011), (-0.618815, 0.785531, -0.002958), (-0.003677, -0.006662, -0.999971)83.66774, 30.78293, 18.14123

-
Components

#1: Protein
CoA transferase III


Mass: 42505.445 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv3272 / Production host: Escherichia coli (E. coli) / References: UniProt: P96877
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.2 %
Description: Plate shaped crystals grown overnight at room temperature
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100mM Tris-HCl, 100mM MgCl2, 20-25% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9858 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 25, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9858 Å / Relative weight: 1
ReflectionResolution: 2.79→43.59 Å / Num. obs: 45755 / % possible obs: 96.88 % / Redundancy: 3.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.1032 / Net I/σ(I): 7.86
Reflection shellResolution: 2.79→2.89 Å / Redundancy: 2.97 % / Rmerge(I) obs: 0.3565 / Mean I/σ(I) obs: 2.97 / Num. unique obs: 4303 / CC1/2: 0.92 / % possible all: 79.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VJQ

2vjq


Resolution: 2.79→43.59 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.898 / Cross valid method: THROUGHOUT / ESU R Free: 0.442 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28578 2260 4.9 %RANDOM
Rwork0.23124 ---
obs0.23387 43495 96.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.566 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20.17 Å2
2--2.13 Å20 Å2
3----1.43 Å2
Refinement stepCycle: 1 / Resolution: 2.79→43.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12467 0 0 143 12610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01912702
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.94917374
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.36251732
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.1424.332494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.796151688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9251574
X-RAY DIFFRACTIONr_chiral_restr0.1020.22044
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0219825
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6086.5676991
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.3039.8338702
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.496.3235709
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.81560.46152225
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A6460.22
12B6460.22
21A6200.22
22C6200.22
31A6640.24
32D6640.24
41B6960.21
42C6960.21
51B7200.21
52D7200.21
61B6860.24
62E6860.24
71C7000.22
72D7000.22
81C6600.22
82E6600.22
91D6880.24
92E6880.24
LS refinement shellResolution: 2.792→2.864 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 119 -
Rwork0.309 2478 -
obs--75.82 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more